diff --git a/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java b/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java
new file mode 100644
index 000000000..ada006e07
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java
@@ -0,0 +1,25 @@
+package org.broadinstitute.sting.gatk.io;
+
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMFileHeader;
+
+/**
+ * A writer that will allow unsorted BAM files to be written
+ * and sorted on-the-fly.
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+public interface StingSAMFileWriter extends SAMFileWriter {
+    /**
+     * Writes the given custom header to SAM file output.
+     * @param header The header to write.
+     */
+    public void writeHeader(SAMFileHeader header);
+
+    /**
+     * Set Whether the BAM file to create is actually presorted.
+     * @param presorted True if the BAM file is presorted.  False otherwise.
+     */    
+    public void setPresorted(boolean presorted);
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
index ea3d61d4f..2b5cf2b8c 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
@@ -49,19 +49,19 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
     public SAMFileWriterStorage( SAMFileWriterStub stub, File file ) {
         this.file = file;
         if( stub.getCompressionLevel() != null )
-            this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getSAMFileHeader(), true, file, stub.getCompressionLevel() );
+            this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getFileHeader(), stub.isPresorted(), file, stub.getCompressionLevel() );
         else
-            this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getSAMFileHeader(), true, file );
-    }
-
-    public void addAlignment( SAMRecord read ) {
-        writer.addAlignment(read);
+            this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getFileHeader(), stub.isPresorted(), file );
     }
 
     public SAMFileHeader getFileHeader() {
         return writer.getFileHeader();
     }
 
+    public void addAlignment( SAMRecord read ) {
+        writer.addAlignment(read);
+    }
+
     public void close() {
         writer.close();
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
index 89972929b..ced17f06e 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
@@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.io.stubs;
 import org.broadinstitute.sting.utils.cmdLine.*;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import net.sf.samtools.SAMFileWriter;
 
 import java.util.List;
@@ -60,7 +61,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
 
     @Override
     public boolean supports( Class type ) {
-        return SAMFileWriter.class.isAssignableFrom(type);
+        return SAMFileWriter.class.equals(type) || StingSAMFileWriter.class.equals(type);
     }
 
     @Override
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
index 3d22f46fb..8512f9873 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
@@ -32,6 +32,7 @@ import net.sf.samtools.SAMFileHeader;
 import java.io.File;
 
 import org.broadinstitute.sting.gatk.io.OutputTracker;
+import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 
 /**
@@ -40,12 +41,17 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
  * @author mhanna
  * @version 0.1
  */
-public class SAMFileWriterStub implements Stub<SAMFileWriter>, SAMFileWriter {
+public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWriter {
     /**
      * Engine to use for collecting attributes for the output SAM file.
      */
     private final GenomeAnalysisEngine engine;
 
+    /**
+     * A header supplied by the user that overrides the merged header from the input BAM.
+     */
+    private SAMFileHeader headerOverride = null;
+
     /**
      * The sam file that this stub should write to.  Should be passed along to
      * whatever happens to create the StreamConnector.
@@ -57,6 +63,11 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, SAMFileWriter {
      */
     private Integer compressionLevel = null;
 
+    /**
+     * Should this BAM be presorted?
+     */
+    private boolean presorted = true;
+
     /**
      * Connects this stub with an external stream capable of serving the
      * requests of the consumer of this stub.
@@ -66,7 +77,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, SAMFileWriter {
     /**
      * Create a new stub given the requested SAM file and compression level.
      * @param engine source of header data, maybe other data about input files.
-     * @param samFile SAM file to (ultimately) cerate.
+     * @param samFile SAM file to (ultimately) create.
      */
     public SAMFileWriterStub( GenomeAnalysisEngine engine, File samFile ) {
         this.engine = engine;
@@ -85,12 +96,8 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, SAMFileWriter {
      * Retrieves the header to use when creating the new SAM file.
      * @return header to use when creating the new SAM file.
      */
-    public SAMFileHeader getSAMFileHeader() {
-        return engine.getSAMFileHeader();    
-    }
-
     public SAMFileHeader getFileHeader() {
-        return getSAMFileHeader();
+        return headerOverride != null ? headerOverride : engine.getSAMFileHeader();
     }
 
     /**
@@ -109,6 +116,22 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, SAMFileWriter {
         this.compressionLevel = compressionLevel;
     }
 
+    /**
+     * Whether the BAM file to create is actually presorted.
+     * @return True if the BAM file is presorted.  False otherwise.
+     */
+    public boolean isPresorted() {
+        return this.presorted;
+    }
+
+    /**
+     * Set Whether the BAM file to create is actually presorted.
+     * @param presorted True if the BAM file is presorted.  False otherwise.
+     */
+    public void setPresorted(boolean presorted) {
+        this.presorted = presorted;
+    }
+
     /**
      * Registers the given streamConnector with this stub.
      * @param outputTracker The connector used to provide an appropriate stream.
@@ -117,6 +140,14 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, SAMFileWriter {
         this.outputTracker = outputTracker;
     }
 
+    /**
+     * Use the given header as the target for this writer.
+     * @param header The header to write.
+     */
+    public void writeHeader(SAMFileHeader header) {
+        this.headerOverride = header;
+    }
+
     /**
      * @{inheritDoc}
      */
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
index a35f7484f..d11ae8d0c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
@@ -8,6 +8,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 
 import java.util.*;
 import java.util.regex.Pattern;
@@ -26,7 +27,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
      * an optional argument to dump the reads out to a BAM file
      */
     @Argument(fullName = "outputBam", shortName = "ob", doc = "Write output to this BAM filename instead of STDOUT", required = false)
-    String outputBamFile = null;
+    StingSAMFileWriter outputBam = null;
 
     @Argument(fullName = "qTrimmingThreshold", shortName = "QT", doc = "", required = false)
     int qTrimmingThreshold = -1;
@@ -117,6 +118,8 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
                 }
             }
         }
+
+        outputBam.setPresorted(clippingRepresentation != ClippingRepresentation.SOFTCLIP_BASES);
     }
 
     /**
@@ -277,23 +280,15 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
      * @return
      */
     public ClippingData reduceInit() {
-        SAMFileWriter outputBam = null;
-
-        if ( outputBamFile != null ) {
-            SAMFileHeader header = this.getToolkit().getSAMFileHeader();
-            boolean maintainsSort = clippingRepresentation != ClippingRepresentation.SOFTCLIP_BASES;
-            outputBam = Utils.createSAMFileWriterWithCompression(header, maintainsSort, outputBamFile, 5);
-        }
-
-        return new ClippingData(outputBam, sequencesToClip);
+        return new ClippingData(sequencesToClip);
     }
 
     public ClippingData reduce(ReadClipper clipper, ClippingData data) {
         if ( clipper == null )
             return data;
 
-        if (data.output != null) {
-            data.output.addAlignment(clipper.clipRead(clippingRepresentation));
+        if (outputBam != null) {
+            outputBam.addAlignment(clipper.clipRead(clippingRepresentation));
         } else {
             out.println(clipper.clipRead(clippingRepresentation).format());
         }
@@ -321,9 +316,6 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
     }
 
     public void onTraversalDone(ClippingData data) {
-        if (data.output != null)
-            data.output.close();
-
         out.printf(data.toString());
     }
 
@@ -522,8 +514,6 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
     }
 
     public class ClippingData {
-        public SAMFileWriter output = null;
-
         public long nTotalReads = 0;
         public long nTotalBases = 0;
         public long nClippedReads = 0;
@@ -534,8 +524,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
 
         HashMap<String, Long> seqClipCounts = new HashMap<String, Long>();
 
-        public ClippingData(SAMFileWriter output, List<SeqToClip> clipSeqs) {
-            this.output = output;
+        public ClippingData(List<SeqToClip> clipSeqs) {
             for (SeqToClip clipSeq : clipSeqs) {
                 seqClipCounts.put(clipSeq.seq, 0L);
             }